Microbial succession and flavour production in the fermented dairy beverage kefir

Kefir is a putatively health-promoting dairy beverage that is produced when a kefir grain, consisting of a consortium of microorganisms, is added to milk to initiate a natural fermentation. Here, a detailed analysis was carried out to determine how the microbial population, gene content and flavour of three kefirs from distinct geographical locations change over the course of 24-hour-fermentations. Metagenomic sequencing revealed that Lactobacillus kefiranofaciens was the dominant bacterial species in kefir during early stages of fermentations, but that Leuconostoc mesenteroides became more prevalent in later stages. This pattern is consistent with an observation that genes involved in aromatic amino acid biosynthesis were absent from Lb. kefiranofaciens, but were present in L. mesenteroides. Additionally, these shifts in the microbial community structure, and associated pathways, corresponded to changes in the levels of volatile compounds. Specifically, Acetobacter spp. correlated with acetic acid, Lactobacillus spp. correlated with carboxylic acids, esters and ketones, Leuconostoc spp. correlated with acetic acid and 2,3-butanedione, and Saccharomyces spp. correlated with esters. The correlation data suggest a causal relationship between microbial taxa and flavour which is supported by observations that addition of Lb. kefiranofaciens NCFB 2797 increased the levels of esters and ketones, whereas addition of L. mesenteroides 213M0 increased acetic acid and 2,3-butanedione. Finally, we detected genes associated with probiotic functionalities in the kefir microbiome. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein, and can be applied to optimise fermentation processes, flavours and health-related attributes of this and other fermented foods.